Comparison of five bacterial strains producing siderophores with ability to chelate iron under alkaline conditions

Siderophores and metallophores: Metal complexation weapons to fight environmental pollution

Siderophores are small molecules of organic nature, released by bacteria to chelate iron from the surrounding environment and subsequently incorporate it into the cytoplasm. In addition to iron, these secondary metabolites can complex with a wide variety of metals, which is why they are commonly studied in the environment. Heavy metals can be very toxic when present in large amounts on the planet, affecting public health and all living organisms. The pollution caused by these toxic metals is increasing, and therefore it is urgent to find practical, sustainable, and economical solutions for remediation. One of the strategies is siderophore-assisted bioremediation, an innovative and advantageous alternative for various environmental applications. This research highlights the various uses of siderophores and metallophores in the environment, underscoring their significance to ecosystems. The study delves into the utilization of siderophores and metallophores in both marine and terrestrial settings (e.g. bioremediation, biocontrol of pathogens, and plant growth promotion), such as bioremediation, biocontrol of pathogens, and plant growth promotion, providing context for the different instances outlined in the existing literature and highlighting their relevance in each field. The study delves into the structures and types of siderophores focusing on their singular characteristics for each application and methodologies used. Focusing on recent developments over the last two decades, the opportunities and challenges associated with siderophores and metallophores applications in the environment were mapped to arm researchers in the fight against environmental pollution.

Production of the siderophore lysochelin in rich media through maltose-promoted high-density growth of Lysobacter sp. 3655

Siderophores are produced by bacteria in iron-restricted conditions. However, we found maltose could induce the biosynthesis of the siderophore lysochelin in Lysobacter sp. 3655 in rich media that are not compatible with siderophore production. Maltose markedly promoted cell growth, with over 300% increase in cell density (OD600) when LB medium was added with maltose (LBM). While lysochelin was not detectable when OD600 in LBM was below 5.0, the siderophore was clearly produced when OD600 reached 7.5 and dramatically increased when OD600 was 15.0. Coincidently, the transcription of lysochelin biosynthesis genes was remarkably enhanced following the increase of OD600. Conversely, the iron concentration in the cell culture dropped to 1.2 μM when OD600 reached 15.0, which was 6-fold lower than that in the starting medium. Moreover, mutants of the maltose-utilizing genes (orf2677 and orf2678) or quorum-sensing related gene orf644 significantly lowered the lysochelin yield. Transcriptomics analysis showed that the iron-utilizing/up-taking genes were up-regulated under high cell density. Accordingly, the transcription of lysochelin biosynthetic genes and the yield of lysochelin were stimulated when the iron-utilizing/up-taking genes were deleted. Finally, lysochelin biosynthesis was positively regulated by a TetR regulator (ORF3043). The lysochelin yield in orf3043 mutant decreased to 50% of that in the wild type and then restored in the complementary strain. Together, this study revealed a previously unrecognized mechanism for lysochelin biosynthetic regulation, by which the siderophore could still be massively produced in Lysobacter even grown in a rich culture medium. This finding could find new applications in large-scale production of siderophores in bacteria.

A Practical Toolkit for the Detection, Isolation, Quantification, and Characterization of Siderophores and Metallophores in Microorganisms

Siderophores are well-recognized low-molecular-weight compounds produced by numerous microorganisms to acquire iron from the surrounding environments. These secondary metabolites can form complexes with other metals besides iron, forming soluble metallophores; because of that, they are widely investigated in either the medicinal or environmental field. One of the bottlenecks of siderophore research is related to the identification of new siderophores from microbial sources. Herein we have compiled a comprehensive range of standard and updated methodologies that have been developed over the past few years to provide a comprehensive toolbox in this area to current researchers.

Exploring the interplay between the core microbiota, physicochemical factors, agrobiochemical cycles in the soil of the historic tokaj mád wine region

A Hungarian survey of Tokaj-Mád vineyards was conducted. Shotgun metabarcoding was applied to decipher the microbial-terroir. The results of 60 soil samples showed that there were three dominant fungal phyla, Ascomycota 66.36% ± 15.26%, Basidiomycota 18.78% ± 14.90%, Mucoromycota 11.89% ± 8.99%, representing 97% of operational taxonomic units (OTUs). Mutual interactions between microbiota diversity and soil physicochemical parameters were revealed. Principal component analysis showed descriptive clustering patterns of microbial taxonomy and resistance gene profiles in the case of the four historic vineyards (Szent Tamás, Király, Betsek, Nyúlászó). Linear discriminant analysis effect size was performed, revealing pronounced shifts in community taxonomy based on soil physicochemical properties. Twelve clades exhibited the most significant shifts (LDA > 4.0), including the phyla Verrucomicrobia, Bacteroidetes, Chloroflexi, and Rokubacteria, the classes Acidobacteria, Deltaproteobacteria, Gemmatimonadetes, and Betaproteobacteria, the order Sphingomonadales, Hypomicrobiales, as well as the family Sphingomonadaceae and the genus Sphingomonas. Three out of the four historic vineyards exhibited the highest occurrences of the bacterial genus Bradyrhizobium, known for its positive influence on plant development and physiology through the secretion of steroid phytohormones. During ripening, the taxonomical composition of the soil fungal microbiota clustered into distinct groups depending on altitude, differences that were not reflected in bacteriomes. Network analyses were performed to unravel changes in fungal interactiomes when comparing postveraison and preharvest samples. In addition to the arbuscular mycorrhiza Glomeraceae, the families Mycosphaerellacae and Rhyzopodaceae and the class Agaricomycetes were found to have important roles in maintaining soil microbial community resilience. Functional metagenomics showed that the soil Na content stimulated several of the microbiota-related agrobiogeochemical cycles, such as nitrogen and sulphur metabolism; steroid, bisphenol, toluene, dioxin and atrazine degradation and the synthesis of folate.

Enhancing phosphate-solubilising microbial communities through artificial selection

Microbial communities, acting as key drivers of ecosystem processes, harbour immense potential for sustainable agriculture practices. Phosphate-solubilising microorganisms, for example, can partially replace conventional phosphate fertilisers, which rely on finite resources. However, understanding the mechanisms and engineering efficient communities poses a significant challenge. In this study, we employ two artificial selection methods, environmental perturbation, and propagation, to construct phosphate-solubilising microbial communities. To assess trait transferability, we investigate the community performance in different media and a hydroponic system with Chrysanthemum indicum. Our findings reveal a distinct subset of phosphate-solubilising bacteria primarily dominated by Klebsiella and Enterobacterales. The propagated communities consistently demonstrate elevated levels of phosphate solubilisation, surpassing the starting soil community by 24.2% in activity. The increased activity of propagated communities remains consistent upon introduction into the hydroponic system. This study shows the efficacy of community-level artificial selection, particularly through propagation, as a tool for successfully modifying microbial communities to enhance phosphate solubilisation.

Microbial dynamics in soils of the Damma glacier forefield show succession in the functional genetic potential

Glacier retreat is a visible consequence of climate change worldwide. Although taxonomic change of the soil microbiomes in glacier forefields have been widely documented, how microbial genetic potential changes along succession is little known. Here, we used shotgun metagenomics to analyse whether the soil microbial genetic potential differed between four stages of soil development (SSD) sampled along three transects in the Damma glacier forefield (Switzerland). The SSDs were characterized by an increasing vegetation cover, from barren soil, to biological soil crust, to sparsely vegetated soil and finally to vegetated soil. Results suggested that SSD significantly influenced microbial genetic potential, with the lowest functional diversity surprisingly occurring in the vegetated soils. Overall, carbohydrate metabolism and secondary metabolite biosynthesis genes overrepresented in vegetated soils, which could be partly attributed to plant-soil feedbacks. For C degradation, glycoside hydrolase genes enriched in vegetated soils, while auxiliary activity and carbohydrate esterases genes overrepresented in barren soils, suggested high labile C degradation potential in vegetated, and high recalcitrant C degradation potential in barren soils. For N-cycling, organic N degradation and synthesis genes dominated along succession, and gene families involved in nitrification were overrepresented in barren soils. Our study provides new insights into how the microbial genetic potential changes during soil formation along the Damma glacier forefield.

Optimization of Siderophore Production in Three Marine Bacterial Isolates along with Their Heavy-Metal Chelation and Seed Germination Potential Determination

Siderophores are low-molecular-weight and high-affinity molecules produced by bacteria under iron-limited conditions. Due to the low iron (III) (Fe+3) levels in surface waters in the marine environment, microbes produce a variety of siderophores. In the current study, halophilic bacteria Bacillus taeanensis SMI_1, Enterobacter sp., AABM_9, and Pseudomonas mendocina AMPPS_5 were isolated from marine surface water of Kalinga beach, Bay of Bengal (Visakhapatnam, Andhra Pradesh, India) and were investigated for siderophore production using the Chrome Azurol S (CAS) assay. The effect of various production parameters was also studied. The optimum production of siderophores for SMI_1 was 93.57% siderophore units (SU) (after 48 h of incubation at 30 °C, pH 8, sucrose as carbon source, sodium nitrate as nitrogen source, 0.4% succinic acid), and for AABM_9, it was 87.18 %SU (after 36 h of incubation period at 30 °C, pH 8, in the presence of sucrose, ammonium sulfate, 0.4% succinic acid). The maximum production of siderophores for AMPPS_5 was 91.17 %SU (after 36 h of incubation at 35 °C, pH 8.5, glucose, ammonium sulfate, 0.4% citric acid). The bacterial isolates SMI_1, AABM_9, and AMPPS_5 showed siderophore production at low Fe+3 concentrations of 0.10 µM, 0.01 µM, and 0.01 µM, respectively. The SMI_1 (73.09 %SU) and AMPPS_5 (68.26 %SU) isolates showed siderophore production in the presence of Zn+2 (10 µM), whereas AABM_9 (50.4 %SU) exhibited siderophore production in the presence of Cu+2 (10 µM). Additionally, these bacterial isolates showed better heavy-metal chelation ability and rapid development in seed germination experiments. Based on these results, the isolates of marine-derived bacteria effectively produced the maximum amount of siderophores, which could be employed in a variety of industrial and environmental applications.

Genomic and microbiological analyses of iron acquisition pathways among respiratory and environmental nontuberculous mycobacteria from Hawai'i

As environmental opportunistic pathogens, nontuberculous mycobacteria (NTM) can cause severe and difficult to treat pulmonary disease. In the United States, Hawai'i has the highest prevalence of infection. Rapid growing mycobacteria (RGM) such as Mycobacterium abscessus and M. porcinum and the slow growing mycobacteria (SGM) including M. intracellulare subspecies chimaera are common environmental NTM species and subspecies in Hawai'i. Although iron acquisition is an essential process of many microorganisms, iron acquisition via siderophores among the NTM is not well-characterized. In this study, we apply genomic and microbiological methodologies to better understand iron acquisition via siderophores for environmental and respiratory isolates of M. abscessus, M. porcinum, and M. intracellulare subspecies chimaera from Hawai'i. Siderophore synthesis and transport genes, including mycobactin (mbt), mmpL/S, and esx-3 were compared among 47 reference isolates, 29 respiratory isolates, and 23 environmental Hawai'i isolates. Among all reference isolates examined, respiratory isolates showed significantly more siderophore pertinent genes compared to environmental isolates. Among the Hawai'i isolates, RGM M. abscessus and M. porcinum had significantly less esx-3 and mbt genes compared to SGM M. chimaera when stratified by growth classification. However, no significant differences were observed between the species when grown on low iron culture agar or siderophore production by the chrome azurol S (CAS) assay in vitro. These results indicate the complex mechanisms involved in iron sequestration and siderophore activity among diverse NTM species.

Siderophore-producing Pantoea ferrattrahens sp. nov. isolated from a clinical specimen and Pantoea ferramans sp. nov. isolated from soil at the bottom of a pond

Two Gram-negative facultative anaerobes were isolated from a sepsis patient with pancreatic cancer (strain PAGU 2156T ) and soil at the bottom of a pond (strain PAGU 2198T ), respectively. These two strains formed haloes around the colonies on chrome azurol S agar plates, indicating the production of siderophores. Two isolates assigned to the genus Pantoea based on the 16S rRNA gene were differentiated from established species by using polymorphic taxonomies. Phylogenetic analysis using four housekeeping genes (gyrB, rpoB, atpD, and infB) showed that strain PAGU 2156T is closely related to Pantoea cypripedii LMG 2657T (89.9%) or Pantoea septica LMG 5345T (95.7%). Meanwhile, strain PAGU 2198T formed a single clade with Pantoea rodasii DSM 26611T (93.6%) and Pantoea rwandensis DSM 105076T (93.3%). The average nucleotide identity values obtained from the draft genome assembly showed ≤90.2% between strain PAGU 2156T and closely related species and ≤81.5% between strain PAGU 2198T and closely related species. Based on various phenotypes, biochemical properties, and whole-cell fatty acid composition compared with related species, it was concluded that each strain should be classified as a new species of the genus Pantoea. In this manuscript, Pantoea ferrattrahens sp. nov. and Pantoea ferramans sp. nov. with strain PAGU 2156T (=NBRC 115930T  = CCUG 76757T ) and strain PAGU 2198T (=NBRC 114265T  = CCUG 75151T ) are proposed as each type strain.

Recent advances in PGPR-mediated resilience toward interactive effects of drought and salt stress in plants

The present crisis at hand revolves around the need to enhance plant resilience to various environmental stresses, including abiotic and biotic stresses, to ensure sustainable agriculture and mitigate the impact of climate change on crop production. One such promising approach is the utilization of plant growth-promoting rhizobacteria (PGPR) to mediate plant resilience to these stresses. Plants are constantly exposed to various stress factors, such as drought, salinity, pathogens, and nutrient deficiencies, which can significantly reduce crop yield and quality. The PGPR are beneficial microbes that reside in the rhizosphere of plants and have been shown to positively influence plant growth and stress tolerance through various mechanisms, including nutrient solubilization, phytohormone production, and induction of systemic resistance. The review comprehensively examines the various mechanisms through which PGPR promotes plant resilience, including nutrient acquisition, hormonal regulation, and defense induction, focusing on recent research findings. The advancements made in the field of PGPR-mediated resilience through multi-omics approaches (viz., genomics, transcriptomics, proteomics, and metabolomics) to unravel the intricate interactions between PGPR and plants have been discussed including their molecular pathways involved in stress tolerance. Besides, the review also emphasizes the importance of continued research and implementation of PGPR-based strategies to address the pressing challenges facing global food security including commercialization of PGPR-based bio-formulations for sustainable agricultural.

Metabolically versatile psychrotolerant Antarctic bacterium Pseudomonas sp. ANT_H12B is an efficient producer of siderophores and accompanying metabolites (SAM) useful for agricultural purposes

BACKGROUND

Bacterial siderophores are chelating compounds with the potential of application in agriculture, due to their plant growth-promoting (PGP) properties, however, high production and purification costs are limiting factors for their wider application. Cost-efficiency of the production could be increased by omitting purification processes, especially since siderophores accompanying metabolites (SAM) often also possess PGP traits. In this study, the metabolism versatility of Pseudomonas sp. ANT_H12B was used for the optimization of siderophores production and the potential of these metabolites and SAM was characterized in the context of PGP properties.

RESULTS

The metabolic diversity of ANT_H12B was examined through genomic analysis and phenotype microarrays. The strain was found to be able to use numerous C, N, P, and S sources, which allowed for the design of novel media suitable for efficient production of siderophores in the form of pyoverdine (223.50-512.60 μM). Moreover, depending on the culture medium, the pH of the siderophores and SAM solutions varied from acidic (pH < 5) to alkaline (pH > 8). In a germination test, siderophores and SAM were shown to have a positive effect on plants, with a significant increase in germination percentage observed in beetroot, pea, and tobacco. The PGP potential of SAM was further elucidated through GC/MS analysis, which revealed other compounds with PGP potential, such as indolic acetic acids, organic acids, fatty acids, sugars and alcohols. These compounds not only improved seed germination but could also potentially be beneficial for plant fitness and soil quality.

CONCLUSIONS

Pseudomonas sp. ANT_H12B was presented as an efficient producer of siderophores and SAM which exhibit PGP potential. It was also shown that omitting downstream processes could not only limit the costs of siderophores production but also improve their agricultural potential.

PGPR: the treasure of multifarious beneficial microorganisms for nutrient mobilization, pest biocontrol and plant growth promotion in field crops

Plant growth-promoting rhizobacteria (PGPR) have multifarious beneficial activities for plant growth promotion; act as source of metabolites, enzymes, nutrient mobilization, biological control of pests, induction of disease resistance vis-a-vis bioremediation potentials by phytoextraction and detoxification of heavy metals, pollutants and pesticides. Agrochemicals and synthetic pesticides are currently being utilized widely in all major field crops, thereby adversely affecting human and animal health, and posing serious threats to the environments. Beneficial microorganisms like PGPR could potentially substitute and supplement the toxic chemicals and pesticides with promising application in organic farming leading to sustainable agriculture practices and bioremediation of heavy metal contaminated sites. Among field crops limited bio-formulations have been prepared till now by utilization of PGPR strains having plant growth promotion, metabolites, enzymes, nutrient mobilization and biocontrol activities. The present review contributes comprehensive description of PGPR applications in field crops including commercial, oilseeds, leguminous and cereal crops to further extend the utilization of these potent groups of beneficial microorganisms so that even higher level of crop productivity and quality produce of field crops could be achieved. PGPR and bacteria based commercialized bio-formulations available worldwide for its application in the field crops have been compiled in this review which can be a substitute for the harmful synthetic chemicals. The current knowledge gap and potential target areas for future research have also been projected.

Bacteria Associated with the Roots of Common Bean (Phaseolus vulgaris L.) at Different Development Stages: Diversity and Plant Growth Promotion

Current agricultural methodologies are vulnerable to erratic climate and are dependent on cost-intensive fertilization to ensure high yields. Sustainable practices should be pursued to ensure food security. Phaseolus vulgaris L. is one of the most produced legumes worldwide and may be an alternative to reduce the environmental impact of meat production as a reliable source of high-quality protein. Plant growth-promoting rhizobacteria (PGPR) are emerging as a sustainable option to increase agricultural production. To understand the dynamics between plants and microorganisms, the culturable microbiota of bean roots was isolated and identified at distinct stages of plant development (early and late vegetative growth, flowering, and pod) and root compartments (rhizoplane, endosphere, and nodules). Diversity and abundance of bacteria associated with root compartments differed throughout the plant life cycle. Bacterial plant growth promotion (PGP) and protection abilities (indole-3-acetic acid production, siderophore synthesis, and antifungal activity) were assessed and associated with plant phenology, demonstrating that among the bacteria associated with plant roots, several strains had an active role in the response to plant biological needs at each stage. Several strains stood out for their ability to display one or more PGP traits, being excellent candidates for efficient stage-specific biostimulants for application in precision agriculture.

Characterization of plant growth promoting activities of indigenous bacteria of phosphate mine wastes, a first step toward revegetation

Morocco holds the vast majority of the world's phosphate reserves, but due to the processes involved in extracting and commercializing these reserves, large quantities of de-structured, nutritionally deficient mine phosphate wastes are produced each year. In a semi-arid climate, these wastes severely hamper plant growth and development leading to huge unvegetated areas. Soil indigenous Plant Growth-Promoting Bacteria (PGPB) play a pivotal role in restauration of these phosphate mining wastes by revegetation, by increasing plants development, soil functioning, and nutrient cycling. The development of a vegetative cover above the degraded phosphate wastes, could stabilize and reintegrate these wastes in the surrounding environment. The current study's objectives were to isolate, characterize, and identify indigenous bacterial strains, and test their PGP activity in vitro and, for the best-performing strains in planta, in order to assess their potential for acting as biofertilizers. A quantitative test for the synthesis of auxin and the production of siderophores as well as a qualitative test for the solubilization of phosphate were performed on all isolated bacterial strains. The production of hydrogen cyanide (HCN), exopolysaccharides (EPS), and enzymes were also examined. Three bacteria, selected among the best PGPB of this study, were tested in planta to determine whether such indigenous bacteria could aid plant growth in this de-structured and nutrient-poor mining soil. Using 16S rRNA gene sequencing, 41 bacterial strains were isolated and 11 genera were identified: Acinetobacter, Agrococcus, Bacillus, Brevibacterium, Microbacterium, Neobacillus, Paenibacillus, Peribacillus, Pseudarthrobacter, Stenotrophomonas, and Raoultella. Among the three best performing bacteria (related to Bacillus paramycoides, Brevibacterium anseongense, and Stenotrophomonas rhizophila), only Stenotrophomonas rhizophila and Brevibacterium anseongense were able to significantly enhance Lupinus albus L. growth. The best inoculation results were obtained using the strain related to Stenotrophomonas rhizophila, improving the plant's root dry weight and chlorophyll content. This is also, to our knowledge, the first study to show a PGP activity of Brevibacterium anseongense.

Application of data integration for rice bacterial strain selection by combining their osmotic stress response and plant growth-promoting traits

Agricultural application of plant-beneficial bacteria to improve crop yield and alleviate the stress caused by environmental conditions, pests, and pathogens is gaining popularity. However, before using these bacterial strains in plant experiments, their environmental stress responses and plant health improvement potential should be examined. In this study, we explored the applicability of three unsupervised machine learning-based data integration methods, including principal component analysis (PCA) of concatenated data, multiple co-inertia analysis (MCIA), and multiple kernel learning (MKL), to select osmotic stress-tolerant plant growth-promoting (PGP) bacterial strains isolated from the rice phyllosphere. The studied datasets consisted of direct and indirect PGP activity measurements and osmotic stress responses of eight bacterial strains previously isolated from the phyllosphere of drought-tolerant rice cultivar. The production of phytohormones, such as indole-acetic acid (IAA), gibberellic acid (GA), abscisic acid (ABA), and cytokinin, were used as direct PGP traits, whereas the production of hydrogen cyanide and siderophore and antagonistic activity against the foliar pathogens Pyricularia oryzae and Helminthosporium oryzae were evaluated as measures of indirect PGP activity. The strains were subjected to a range of osmotic stress levels by adding PEG 6000 (0, 11, 21, and 32.6%) to their growth medium. The results of the osmotic stress response experiments showed that all bacterial strains accumulated endogenous proline and glycine betaine (GB) and exhibited an increase in growth, when osmotic stress levels were increased to a specific degree, while the production of IAA and GA considerably decreased. The three applied data integration methods did not provide a similar grouping of the strains. Especially deviant was the ordination of microbial strains based on the PCA of concatenated data. However, all three data integration methods indicated that the strains Bacillus altitudinis PB46 and B. megaterium PB50 shared high similarity in PGP traits and osmotic stress response. Overall, our results indicate that data integration methods complement the single-table data analysis approach and improve the selection process for PGP microbial strains.

Bacterial Siderophores: Classification, Biosynthesis, Perspectives of Use in Agriculture

Siderophores are synthesized and secreted by many bacteria, yeasts, fungi, and plants for Fe (III) chelation. A variety of plant-growth-promoting bacteria (PGPB) colonize the rhizosphere and contribute to iron assimilation by plants. These microorganisms possess mechanisms to produce Fe ions under iron-deficient conditions. Under appropriate conditions, they synthesize and release siderophores, thereby increasing and regulating iron bioavailability. This review focuses on various bacterial strains that positively affect plant growth and development through synthesizing siderophores. Here we discuss the diverse chemical nature of siderophores produced by plant root bacteria; the life cycle of siderophores, from their biosynthesis to the Fe-siderophore complex degradation; three mechanisms of siderophore biosynthesis in bacteria; the methods for analyzing siderophores and the siderophore-producing activity of bacteria and the methods for screening the siderophore-producing activity of bacterial colonies. Further analysis of biochemical, molecular-biological, and physiological features of siderophore synthesis by bacteria and their use by plants will allow one to create effective microbiological preparations for improving soil fertility and increasing plant biomass, which is highly relevant for sustainable agriculture.

Fundaments and Concepts on Screening of Microorganisms for Biotechnological Applications. Mini Review

Microbial biotechnology uses microorganisms and their derivatives to generate industrial and/or environmental products that impact daily life. Modern biotechnology uses proteomics, metabolomics, quantum processors, and massive sequencing methods to yield promising results with microorganisms. However, the fundamental concepts of microbial biotechnology focus on the specific search for microorganisms from natural sources and their correct analysis to implement large-scale processes. This mini-review focuses on the methods used for the isolation and selection of microorganisms with biotechnological potential to empathize the importance of these concepts in microbial biotechnology. In this work, a review of the state of the art in recent years on the selection and characterization of microorganisms with a basic approach to understanding the importance of fundamental concepts in the field of biotechnology was carried out. The proper selection of isolation sources and the design of suitable selection criteria according to the desired activity have generated substantial changes in the development of biotechnology for more than three decades. Some examples include Taq polymerase in the PCR method and CRISPR technology. The objective of this mini review is to establish general ideas for the screening of microorganisms based on basic concepts of biotechnology that are left aside in several articles and maintain the importance of the basic concepts that this implies in the development of modern biotechnology.

Physiological and Transcriptome Analyses Revealed the Mechanism by Which Deferoxamine Promotes Iron Absorption in Cinnamomum camphora

Iron deficiency causes chlorosis and growth inhibition in Cinnamomum camphora, an important landscaping tree species. Siderophores produced by plant growth-promoting rhizobacteria have been widely reported to play an indispensable role in plant iron nutrition. However, little to date has been determined about how microbial siderophores promote plant iron absorption. In this study, multidisciplinary approaches, including physiological, biochemical and transcriptome methods, were used to investigate the role of deferoxamine (DFO) in regulating Fe availability in C. camphora seedlings. Our results showed that DFO supplementation significantly increased the Fe²⁺ content, SPAD value and ferric-chelate reductase (FCR) activity in plants, suggesting its beneficial effect under Fe deficiency. This DFO-driven amelioration of Fe deficiency was further supported by the improvement of photosynthesis. Intriguingly, DFO treatment activated the metabolic pathway of glutathione (GSH) synthesis, and exogenous spraying reduced glutathione and also alleviated chlorosis in C. camphora. In addition, the expression of some Fe acquisition and transport-related genes, including CcbHLH, CcFRO6, CcIRT2, CcNramp5, CcOPT3 and CcVIT4, was significantly upregulated by DFO treatment. Collectively, our data demonstrated an effective, economical and feasible organic iron-complexing agent for iron-deficient camphor trees and provided new insights into the mechanism by which siderophores promote iron absorption in plants.

Exogenous Melatonin Reprograms the Rhizosphere Microbial Community to Modulate the Responses of Barley to Drought Stress

The rhizospheric melatonin application-induced drought tolerance has been illuminated in various plant species, while the roles of the rhizosphere microbial community in this process are still unclear. Here, the diversity and functions of the rhizosphere microbial community and related physiological parameters were tested in barley under the rhizospheric melatonin application and drought. Exogenous melatonin improved plant performance under drought via increasing the activities of non-structural carbohydrate metabolism enzymes and activating the antioxidant enzyme systems in barley roots under drought. The 16S/ITS rRNA gene sequencing revealed that drought and melatonin altered the compositions of the microbiome. Exogenous melatonin increased the relative abundance of the bacterial community in carbohydrate and carboxylate degradation, while decreasing the relative abundance in the pathways of fatty acid and lipid degradation and inorganic nutrient metabolism under drought. These results suggest that the effects of melatonin on rhizosphere microbes and nutrient condition need to be considered in its application for crop drought-resistant cultivation.

Characterization of an Endophytic Antagonistic Bacterial Strain Bacillus halotolerans LBG-1-13 with Multiple Plant Growth-Promoting Traits, Stress Tolerance, and Its Effects on Lily Growth

Microbial inoculants are an important tool for increasing arable land productivity and decreasing mineral fertilizer application. This study was aimed at isolating and identifying endophytic antagonistic bacteria from lily (Lilium davidii var. unicolor) roots grown in Northwestern China and at evaluating their antifungal activity and plant growth-promoting characteristics. For this purpose, endophytic bacteria were isolated from plant roots, and plant growth-promoting strains were identified. One bacterial strain, isolated from the root part, was identified as Bacillus halotolerans based on 16S rRNA gene sequence analysis and was designated as LBG-1-13. The strain showed antagonistic activities against important plant pathogens of lily including Botrytis cinerea, Botryosphaeria dothidea, and Fusarium oxysporum. The highest percentage of growth inhibition, i.e., 71.65 ± 2.39%, was observed for LBG-1-13 against Botryosphaeria dothidea followed by 68.33 ± 4.70% and 48.22 ± 4.11% against Botrytis cinerea and Fusarium oxysporum, respectively. Meanwhile, the isolated strain also showed plant growth-promoting traits such as the production of indole-3-acetic acid (IAA), siderophore, ACC deaminase, and phosphate solubilization activity. The strain showed ACC deaminase activity and was able to cleave 58.41 ± 2.62 nmol α-ketobutyrate (mg protein)⁻¹ min⁻¹. The strain exhibited tolerance to salt and drought stress in an in vitro experiment. The strain LBG-1-13 was able to grow in the presence of 10% NaCl and 20% polyethylene glycol (PEG) in the growth medium. Inoculation of Lilium varieties, Tresor and Bright Diamond, with LBG-1-13 enhanced plant growth under greenhouse and field conditions, respectively. All these results demonstrated that Bacillus halotolerans LBG-1-13 could be utilized as a good candidate in the biocontrol of lily disease and plant growth promotion in sustainable agriculture.

Plant Growth-Promoting Rhizobacteria Eliminate the Effect of Drought Stress in Plants: A Review

Plants evolve diverse mechanisms to eliminate the drastic effect of biotic and abiotic stresses. Drought is the most hazardous abiotic stress causing huge losses to crop yield worldwide. Osmotic stress decreases relative water and chlorophyll content and increases the accumulation of osmolytes, epicuticular wax content, antioxidant enzymatic activities, reactive oxygen species, secondary metabolites, membrane lipid peroxidation, and abscisic acid. Plant growth-promoting rhizobacteria (PGPR) eliminate the effect of drought stress by altering root morphology, regulating the stress-responsive genes, producing phytohormones, osmolytes, siderophores, volatile organic compounds, and exopolysaccharides, and improving the 1-aminocyclopropane-1-carboxylate deaminase activities. The use of PGPR is an alternative approach to traditional breeding and biotechnology for enhancing crop productivity. Hence, that can promote drought tolerance in important agricultural crops and could be used to minimize crop losses under limited water conditions. This review deals with recent progress on the use of PGPR to eliminate the harmful effects of drought stress in traditional agriculture crops.

Application of microbe-impregnated tannery solid waste biochar in soil enhances growth performance of sunflower

Synergistic effect of biochar and microbes in soil enhances performance of plants. Hazardous tannery solid waste can be reduced by one-third in volume by conversion to biochar. A greenhouse trial was set up with soil having different doses of metal resistant microbe-impregnated biochar (MIBC) prepared from tannery solid waste. Consortia of autochthonous strains of Trichoderma and Bacillus were inoculated on BC and the behavior and fate of metals were evaluated for their bioavailability to sunflower. Sunflower was grown in pots for 80 days having six different amendments of tannery solid waste biochar (0-10% w/w) with and without Trichoderma and Bacillus consortia and its morphological and biochemical attributes as well as metal uptake were observed. The results illustrated that application of BC at 2% rate without inoculation increased the shoot length and dry biomass by 19.8% and 77.4%, respectively, while plant growth and performance were reduced at higher amendments of BC. However, application of MIBC with Trichoderma or/and Bacillus consortium significantly improved the plant attributes at all levels of amendment. The results indicated that MIBC having Trichoderma and Bacillus consortia at 10% rate increased shoot length and dry biomass by 65.3% and 516% compared to control without BC. Application of BC without inoculation reduced the uptake of Cu, Fe, and Ni and increased the mobilization of all other metals for uptake in sunflower. Mobilization and uptake of Cd, Cr, Cu, Ni, Pb, and Zn decreased with MIBC having Trichoderma and Bacillus consortia whereas that of Fe and Mg were noted. A considerable decrease in proline and total phenolic content was demonstrated by MIBC-grown sunflower. The data of metal fractionation in BC also supported the above findings. Therefore, MIBC can be used as a promising option for enhancing growth performance and ensuring the physiological safety of sunflower as an energy crop.

Production and Potential Genetic Pathways of Three Different Siderophore Types in Streptomyces tricolor Strain HM10

Siderophores are iron-chelating low-molecular-weight compounds that bind iron (Fe3+) with a high affinity for transport into the cell. The newly isolated strain Streptomyces tricolor HM10 secretes a pattern of secondary metabolites. Siderophore molecules are the representatives of such secondary metabolites. S. tricolor HM10 produces catechol, hydroxamate, and carboxylate types of siderophores. Under 20 μM FeCl3 conditions, S. tricolor HM10 produced up to 6.00 µg/mL of catechol siderophore equivalent of 2,3-DHBA (2,3-dihydroxybenzoic acid) after 4 days from incubation. In silico analysis of the S. tricolor HM10 genome revealed three proposed pathways for siderophore biosynthesis. The first pathway, consisting of five genes, predicted the production of catechol-type siderophore similar to petrobactin from Bacillus anthracis str. Ames. The second proposed pathway, consisting of eight genes, is expected to produce a hydroxamate-type siderophore similar to desferrioxamine B/E from Streptomyces sp. ID38640, S. griseus NBRC 13350, and/or S. coelicolor A3(2). The third pathway exhibited a pattern identical to the carboxylate xanthoferrin siderophore from Xanthomonas oryzae. Thus, Streptomyces strain HM10 could produce three different types of siderophore, which could be an incentive to use it as a new source for siderophore production in plant growth-promoting, environmental bioremediation, and drug delivery strategy.

Mechanistic Insights and Potential Use of Siderophores Producing Microbes in Rhizosphere for Mitigation of Stress in Plants Grown in Degraded Land

Plant growth performance under a stressful environment, notably in the agriculture field, is directly correlated with the rapid growth of the human population, which triggers the pressure on crop productivity. Plants perceived many stresses owing to degraded land, which induces low plant productivity and, therefore, becomes a foremost concern for the future to face a situation of food scarcity. Land degradation is a very notable environmental issue at the local, regional, and global levels for agriculture. Land degradation generates global problems such as drought desertification, heavy metal contamination, and soil salinity, which pose challenges to achieving many UN Sustainable Development goals. The plant itself has a varied algorithm for the mitigation of stresses arising due to degraded land; the rhizospheric system of the plant has diverse modes and efficient mechanisms to cope with stress by numerous root-associated microbes. The suitable root-associated microbes and components of root exudate interplay against stress and build adaptation against stress-mediated mechanisms. The problem of iron-deficient soil is rising owing to increasing degraded land across the globe, which hampers plant growth productivity. Therefore, in the context to tackle these issues, the present review aims to identify plant-stress status owing to iron-deficient soil and its probable eco-friendly solution. Siderophores are well-recognized iron-chelating agents produced by numerous microbes and are associated with the rhizosphere. These siderophore-producing microbes are eco-friendly and sustainable agents, which may be managing plant stresses in the degraded land. The review also focuses on the molecular mechanisms of siderophores and their chemistry, cross-talk between plant root and siderophores-producing microbes to combat plant stress, and the utilization of siderophores in plant growth on degraded land.

Perspective on the biotechnological production of bacterial siderophores and their use

Iron (Fe) is an essential element in several fundamental cellular processes. Although present in high amounts in the Earth's crust, Fe can be a scarce element due to its low bioavailability. To mitigate Fe limitation, microorganism (bacteria and fungi) and grass plant biosynthesis and secret secondary metabolites, called siderophores, with capacity to chelate Fe(III) with high affinity and selectivity. This review focuses on the current state of knowledge concerning the production of siderophores by bacteria. The main siderophore types and corresponding siderophore-producing bacteria are summarized. A concise outline of siderophore biosynthesis, secretion and regulation is given. Important aspects to be taken into account in the selection of a siderophore-producing bacterium, such as biological safety, complexing properties of the siderophores and amount of siderophores produced are summarized and discussed. An overview containing recent scientific advances on culture medium formulation and cultural conditions that influence the production of siderophores by bacteria is critically presented. The recovery, purification and processing of siderophores are outlined. Potential applications of siderophores in different sectors including agriculture, environment, biosensors and the medical field are sketched. Finally, future trends regarding the production and use of siderophores are discussed. KEY POINTS : • An overview of siderophore production by bacteria is critically presented • Scientific advances on factors that influence siderophores production are discussed • Potential applications of siderophores, in different fields, are outlined.

Perspective on the biotechnological production of bacterial siderophores and their use

Iron (Fe) is an essential element in several fundamental cellular processes. Although present in high amounts in the Earth's crust, Fe can be a scarce element due to its low bioavailability. To mitigate Fe limitation, microorganism (bacteria and fungi) and grass plant biosynthesis and secret secondary metabolites, called siderophores, with capacity to chelate Fe(III) with high affinity and selectivity. This review focuses on the current state of knowledge concerning the production of siderophores by bacteria. The main siderophore types and corresponding siderophore-producing bacteria are summarized. A concise outline of siderophore biosynthesis, secretion and regulation is given. Important aspects to be taken into account in the selection of a siderophore-producing bacterium, such as biological safety, complexing properties of the siderophores and amount of siderophores produced are summarized and discussed. An overview containing recent scientific advances on culture medium formulation and cultural conditions that influence the production of siderophores by bacteria is critically presented. The recovery, purification and processing of siderophores are outlined. Potential applications of siderophores in different sectors including agriculture, environment, biosensors and the medical field are sketched. Finally, future trends regarding the production and use of siderophores are discussed. KEY POINTS : • An overview of siderophore production by bacteria is critically presented • Scientific advances on factors that influence siderophores production are discussed • Potential applications of siderophores, in different fields, are outlined.

Acidity and availability of aluminum, iron and manganese as factors affecting germination in European acidic dry and alkaline xerothermic grasslands

Germination ecology of 10 species from acidic dry grasslands and 10 species from alkaline xerothermic grasslands was studied. The seeds were subjected to different pH, iron (Fe), manganese (Mn) and aluminum (Al) treatments under controlled conditions. Effects of ionic (chlorides) and chelated forms (HBED chelates) of Fe and Mn were also compared. Final germination percentage (FGP) and index of germination velocity (IGV) were calculated. The results indicate that pH and extremely high availability of Al are the major edaphic filters regulating germination-based revegetation, while availability of Fe and Mn is of the secondary importance. Both chelates and ionic forms of Fe and Mn exerted similar effects on the ability of seeds to complete germination. It suggests that both chelates are not hazardous for early ontogenetic stages of plants. Neither group has group-specific adaptations pertaining to germination characteristics in the context of the studied chemical stimuli, which indicates a diversity of germination strategies and individual species-specific reactions to the tested factors.

Screening of Siderophore-Producing Bacteria and Their Effects on Promoting the Growth of Plants

Iron deficiency is a major global agricultural problem. Siderophores can help organisms to uptake iron in form of siderophore-Fe³⁺ complexes and then in the cell cytosol, iron is reducted and released in ferrous form. This research aimed to obtain some efficient siderophore-producing bacterial strains and evaluate their plant growth-promoting effects in the iron-deficit environment. Two strains, Brucella sp. E7 and Pseudomonas brassicae W7, were isolated from rhizosphere soil. Both strains could produce maximum siderophores under the optimal conditions. Plant promoting experiment showed that many indicators of Vigna radiata seedling were all increased significantly by strain E7/W7 or the consortium of E7 + W7. Under no-iron and high iron stress, the inoculation treatment also showed growth promotion effects on both Vigna radiata and Lolium multiflorum. These results indicated that the potential ability of strain E7 and W7 in increasing agricultural production as a growth-promoting agent in iron-deficit soil.

Bacillus subtilis Impact on Plant Growth, Soil Health and Environment: Dr. Jekyll and Mr. Hyde

The increased dependence of farmers on chemical fertilizers poses a risk to soil fertility and ecosystem stability. Plant growth-promoting rhizobacteria (PGPR) are at the forefront of sustainable agriculture, providing multiple benefits for the enhancement of crop production and soil health. Bacillus subtilis is a common PGPR in soil that plays a key role in conferring biotic and abiotic stress tolerance to plants by induced systemic resistance (ISR), biofilm formation, and lipopeptide production. As a part of bioremediating technologies, Bacillus spp. can purify metal contaminated soil. It acts as a potent denitrifying agent in agroecosystems while improving the carbon sequestration process when applied in a regulated concentration. Although it harbors several antibiotic resistance genes (ARGs), it can reduce the horizontal transfer of ARGs during manure composting by modifying the genetic makeup of existing microbiota. In some instances, it affects the beneficial microbes of the rhizosphere. External inoculation of B. subtilis has both positive and negative impacts on the endophytic and semi-synthetic microbial community. Soil texture, type, pH, and bacterial concentration play a crucial role in the regulation of all these processes. Soil amendments and microbial consortia of Bacillus produced by microbial engineering could be used to lessen the negative effect on soil microbial diversity. The complex plant-microbe interactions could be decoded using transcriptomics, proteomics, metabolomics, and epigenomics strategies which would be beneficial for both crop productivity and the well-being of soil microbiota. Bacillus subtilis has more positive attributes similar to the character of Dr. Jekyll and some negative attributes on plant growth, soil health, and the environment akin to the character of Mr. Hyde.

Phyto-Beneficial Traits of Rhizosphere Bacteria: In Vitro Exploration of Plant Growth Promoting and Phytopathogen Biocontrol Ability of Selected Strains Isolated from Harsh Environments

Beneficial interactions between plants and some bacterial species have been long recognized, as they proved to exert various growth-promoting and health-protective activities on economically relevant crops. In this study, the growth promoting and antifungal activity of six bacterial strains, Paenarthrobacter ureafaciens, Beijerinckia fluminensis, Pseudomonas protegens, Arthrobacter sp., Arthrobacter defluii, and Arthrobacter nicotinovorans, were investigated. The tested strains resulted positive for some plant growth promoting (PGP) traits, such as indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate-deaminase (ACC-deaminase), siderophore production, and solubilization of phosphates. The effect of the selected bacteria on Arabidopsis thaliana seedlings growth was assessed using different morphological parameters. Bacterial activity against the phytopathogenic fungal species Aspergillus flavus, Fusarium proliferatum, and Fusarium verticillioides was also assessed, since these cause major yield losses in cereal crops and are well-known mycotoxin producers. Strains Pvr_9 (B. fluminensis) and PHA_1 (P. protegens) showed an important growth-promoting effect on A. thaliana coupled with a high antifungal activity on all the three fungal species. The analysis of bacterial broths through ultra performance liquid chromatography-mass spectrometry (UPLC-MS) and liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) confirmed the presence of potential PGP-compounds, among these are desferrioxamine B, aminochelin, asperchrome B, quinolobactin siderophores, and salicylic acid.

Bacterial endophytes from ginseng and their biotechnological application

Ginseng has been well-known as a medicinal plant for thousands of years. Bacterial endophytes ubiquitously colonize the inside tissues of ginseng without any disease symptoms. The identification of bacterial endophytes is conducted through either the internal transcribed spacer region combined with ribosomal sequences or metagenomics. Bacterial endophyte communities differ in their diversity and composition profile, depending on the geographical location, cultivation condition, and tissue, age, and species of ginseng. Bacterial endophytes have a significant effect on the growth of ginseng through indole-3-acetic acid (IAA) and siderophore production, phosphate solubilization, and nitrogen fixation. Moreover, bacterial endophytes can protect ginseng by acting as biocontrol agents. Interestingly, bacterial endophytes isolated from Panax species have the potential to produce ginsenosides and bioactive metabolites, which can be used in the production of food and medicine. The ability of bacterial endophytes to transform major ginsenosides into minor ginsenosides using β-glucosidase is gaining increasing attention as a promising biotechnology. Recently, metabolic engineering has accelerated the possibilities for potential applications of bacterial endophytes in producing beneficial secondary metabolites.

Isolation, characterization, and evaluation of a high-siderophore-yielding bacterium from heavy metal-contaminated soil

Heavy metal-resistant siderophore-producing bacteria (SPB) with plant growth-promoting traits can assist in phytoremediation of heavy metal-contaminated soil. We isolated siderophore-producing bacteria from Pb and Zn mine soil in Shangyu, Zhejiang, China. The isolate with the highest siderophore production, strain SX9, was identified as Burkholderia sp. Burkholderia sp. SX9 produced catecholate-type siderophore, with the highest production at a pH range of 6.0 to 8.0, a temperature range of 20 to 30 °C and NaCl concentration below 2%. Siderophore production was highest without Fe³⁺ and became gradually lower with increasing Fe³⁺ concentration. Minimal inhibitory concentrations (MIC) of Pb²⁺, Zn²⁺, Cu²⁺, and Cd²⁺ were 4000, 22000, 5000, and 2000 μmol L^-1, respectively. The strain had a strong metal solubilization ability: the contents of Cu²⁺, Zn²⁺, and Cd²⁺ in the supernatant were 47.4%, 133.0%, and 35.4% higher, respectively, in strain SX9-inoculated cultures than in the not inoculated controls. The siderophore produced by strain SX9 could combine with Fe³⁺, Zn²⁺, and Cd²⁺ with good effectiveness. The plant growth-promoting traits of the strain included indole acetic acid (IAA) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, and phosphate solubilization capability. Compared to the uninoculated growth medium and SX9 culture supernatant, the germination rate of Lolium perenne seeds was higher when inoculated with strain SX9 culture. In the experiment of seed germination, adding bacterial culture or supernatant could alleviate the toxicity of heavy metals to L. perenne seed germination. Under Cu²⁺ and Zn²⁺ stress, strain SX9 promoted the germination rate. Taken together, Burkholderia sp. SX9 had properties beneficial in the microbial enhancement of phytoremediation of soil contaminated with heavy metals.

Harnessing microbial iron chelators to develop innovative therapeutic agents

•

Microbial iron chelators as a new route to develop inspiring antimicrobials.

•

Siderophore-mimicking antibiotics as a pathogen-targeted strategy.

•

Effectiveness of iron chelators on antibiotic-resistant Gram-negative bacteria.

•

Iron chelators and the treatment of iron overload diseases.

•

Iron chelators as powerful tools for cancer therapy.

Background

Aim of Review

Key Scientific Concepts of Review

Epiphytic PGPB Bacillus megaterium AFI1 and Paenibacillus nicotianae AFI2 Improve Wheat Growth and Antioxidant Status under Ni Stress

The present study demonstrates the Ni toxicity-ameliorating and growth-promoting abilities of two different bacterial isolates when applied to wheat (Triticum aestivum L.) as the host plant. Two bacterial strains tolerant to Ni stress were isolated from wheat seeds and selected based on their ability to improve the germination of wheat plants; they were identified as Bacillus megaterium AFI1 and Paenibacillus nicotianae AFI2. The protective effects of these epiphytic bacteria against Ni stress were studied in model experiments with two wheat cultivars: Ni stress-tolerant Leningradskaya 6 and susceptible Chinese spring. When these isolates were used as the inoculants applied to Ni-treated wheat plants, the growth parameters and the levels of photosynthetic pigments of the two wheat cultivars both under normal and Ni-stress conditions were increased, though B. megaterium AFI1 had a more pronounced ameliorative effect on the Ni contents in plant tissues due to its synthesis of siderophores. Over the 10 days of Ni exposure, the plant growth promotion bacteria (PGPB) significantly reduced the lipid peroxidation (LPO), ascorbate peroxidase (APX), superoxide dismutase (SOD) activities and proline content in the leaves of both wheat cultivars. The PGPB also increased peroxidase (POX) activity and the levels of chlorophyll a, chlorophyll b, and carotenoids in the wheat leaves. It was concluded that B. megaterium AFI1 is an ideal candidate for bioremediation and wheat growth promotion against Ni-induced oxidative stress, as it increases photosynthetic pigment contents, induces the antioxidant defense system, and lowers Ni metal uptake.

Prospecting Endophytic Bacteria Endowed With Plant Growth Promoting Potential Isolated From Camellia sinensis

Endophytes are well-acknowledged inoculants to promote plant growth, and extensive research has been done in different plants. However, there is a lacuna about the endophytes associated with tea clones and their benefit to promote plant growth. The present study focuses on isolating and characterizing the beneficial endophytic bacteria (EnB) prevalent in commercially important tea clones cultivated in North Eastern India as plant growth promoters. Diversity of culturable EnB microbiome, in vitro traits for plant growth promotion (PGP), and applicability of potent isolates as bioinoculant for in vivo PGP abilities have been assessed in the present study. A total of 106 EnB identified as members of phyla Proteobacteria, Firmicutes, and Actinobacteria were related to 22 different genera and six major clusters. Regarding PGP traits, the percentage of isolates positive for the production of indole acetic acid, phosphate solubilization, nitrogen fixation siderophore, ammonia, and 1-aminocyclopropane-1-carboxylic acid deaminase production were 86.8, 28.3, 78.3, 30.2, 95.3, and 87.7, respectively. In total, 34.0, 52.8, and 17.0% of EnB showed notable production of hydrolytic enzymes like cellulase, protease, and amylase, respectively. Additionally, based on the bonitur score, the top two isolates K96 identified as Stenotrophomonas sp. and M45 identified as Pseudomonas sp. were evaluated for biofilm formation, motility, and in vivo plant growth promoting activity. Results suggested strong biofilm formation and motility in K96 and M45 which may attribute to the colonization of the strains in the plants. Further in vivo plant growth promotion experiment suggested sturdy efficacy of the K96 and M45 as plant growth promoters in nursery condition in commercial tea clones Tocklai vegetative (TV) TV22 and TV26. Thus, this study emphasizes the opportunity of commercialization of the selected isolates for sustainable development of tea and other crops.

A Taxon-Wise Insight Into Rock Weathering and Nitrogen Fixation Functional Profiles of Proglacial Systems

The Arctic environment is particularly affected by global warming, and a clear trend of the ice retreat is observed worldwide. In proglacial systems, the newly exposed terrain represents different environmental and nutrient conditions compared to later soil stages. Therefore, proglacial systems show several environmental gradients along the soil succession where microorganisms are active protagonists of the soil and carbon pool formation through nitrogen fixation and rock weathering. We studied the microbial succession of three Arctic proglacial systems located in Svalbard (Midtre Lovénbreen), Sweden (Storglaciären), and Greenland (foreland close to Kangerlussuaq). We analyzed 65 whole shotgun metagenomic soil samples for a total of more than 400 Gb of sequencing data. Microbial succession showed common trends typical of proglacial systems with increasing diversity observed along the forefield chronosequence. Microbial trends were explained by the distance from the ice edge in the Midtre Lovénbreen and Storglaciären forefields and by total nitrogen (TN) and total organic carbon (TOC) in the Greenland proglacial system. Furthermore, we focused specifically on genes associated with nitrogen fixation and biotic rock weathering processes, such as nitrogenase genes, obcA genes, and genes involved in cyanide and siderophore synthesis and transport. Whereas we confirmed the presence of these genes in known nitrogen-fixing and/or rock weathering organisms (e.g., Nostoc, Burkholderia), in this study, we also detected organisms that, even if often found in soil and proglacial systems, have never been related to nitrogen-fixing or rock weathering processes before (e.g., Fimbriiglobus, Streptomyces). The different genera showed different gene trends within and among the studied systems, indicating a community constituted by a plurality of organisms involved in nitrogen fixation and biotic rock weathering, and where the latter were driven by different organisms at different soil succession stages.

Comparative phenotypic characterization of hybrid Shiga toxin-producing / uropathogenic Escherichia coli, canonical uropathogenic and Shiga toxin-producing Escherichia coli

Hybrid Shiga toxin (Stx)-producing Escherichia coli (STEC) and uropathogenic E. coli (UPEC) strains are phylogenetically positioned between STEC and UPEC and can cause both diarrhea and urinary tract infections (UTIs). However, their virulence properties and adaptation to different host milieu in comparison to canonical UPEC and STEC strains are unknown. We determined phenotypes of the STEC/UPEC hybrid with respect to virulence including acid resistance, motility, biofilm formation, siderophore production, and adherence to human colonic Caco-2 and bladder T24 cells and compared to phenotypes of commensal strain MG1655, UPEC strain 536, and STEC strains B2F1 and Sakai. Moreover, we assessed the adaptation of the hybrid to artificial urine medium (AUM) and simulated colonic environment medium (SCEM). Overall acid resistance at pH 2.5 was high except in strains B2F1 and hybrid 05-00787 which showed reduced and extremely low acid resistance, respectively. Motility was reduced in hybrid 05-00787 and 09-05501 but strong in the remaining hybrids. While some hybrids showed high biofilm formation in LB, overall biofilm formation in SCEM and AUM were low and non-existent, respectively. All strains tested showed siderophore activity at equilibrium. All strains except MG1655 adhered to Caco-2 cells with the hybrid having similar adherence when compared to 536 but exhibited 2 and 3 times lower adherence when compared to B2F1 and Sakai, respectively. All Stx-producing strains adhered stronger to T24 cells than strains 536 and MG1655. Overall growth in LB, SCEM and AUM was consistent within the hybrid strains, except hybrid 05-00787 which showed significantly different growth patterns. Our data suggest that the hybrid is adapted to both, the intestinal and extraintestinal milieu. Expression of phenotypes typical of intestinal and extraintestinal pathogens thereby supports its potential to cause diarrhea and UTI.

Oak (Quercus robur) Associated Endophytic Paenibacillus sp. Promotes Poplar (Populus spp.) Root Growth In Vitro

Soil fertilization is necessary for high-demand crop production in agriculture and forestry. Our current dependence on chemical fertilizers has significant harmful side effects. Biofertilization using microorganisms is a sustainable way to limit the need for chemical fertilizers in various enterprises. Most plant endophytic bacteria have thus far been unstudied for their plant growth promoting potential and hence present a novel niche for new biofertilizer strains. We isolated English oak (Quercus robur) endophytic bacteria and tested them for plant growth promoting traits (PGPTs) such as nitrogen fixation, phosphate mineralization/solubilization, siderophore and indole-3-acetic acid (IAA) production. We also investigated the effect the selected isolate had on poplar (Populus spp.) microshoot vegetative growth parameters in vitro. In total 48 bacterial strains were isolated, attributed to Bacillus, Delftia, Paenibacillus, Pantoea and Pseudomonas genera. All the isolates displayed at least three PGPTs, with 39.6% of the isolates displaying all five (all were Pseudomonas spp.) and 18.75% displaying four. Based on relative abundance, Paenibacillus sp. isolate was selected for the poplar microshoot inoculation study. The isolate had a significant positive effect on poplar microshoot root growth and development. Two tested poplar genotypes both had increased lateral root number and density, fresh and dry root biomass. Furthermore, one genotype had increased length and number of adventitious roots as well as a decrease in fresh aboveground biomass. The root enhancement was attributed to IAA production. We propose this isolate for further studies as a potential biofertilizer.

Phenetic and Molecular Diversity of Nitrogen Fixating Plant Growth Promoting Azotobacter Isolated from Semiarid Regions of India

In the present study, 24 Azotobacter strains were isolated from soils of different areas of southern Rajasthan and characterized at biochemical, functional, and molecular levels. The isolated Azotobacter strains were gram negative and cyst forming when viewed under the microscope. These strains were also screened for their plant growth promoting activities and the ability of these isolates to survive under abiotic stress conditions viz. salt, pH, temperature, and drought stress. All the isolates showed IAA, siderophore, HCN, and ammonia production, whereas seven Azotobacter strains showed phosphate solubilization. Amplified Ribosomal DNA Restriction Analysis (ARDRA) revealed significant diversity among Azotobacter strains and the dendrogram obtained differentiated twenty-four of the strains into two major clusters at a similarity coefficient of 0.64. Qualitative and quantitative N2 fixation abilities of these strains were also detrained, and the amounts of acetylene reduced by Azotobacter strains were in the range of 1.31 to 846.56 nmol C2H4 mg protein−1 h−1. The strains showing high nitrogen fixation ability with multiple PGP activities were selected for further pot studies, and these Azotobacter strains significantly increased the various plant growth parameters of maize plantlets. Furthermore, the best Azotobacter isolates were subjected to 16S rRNA sequencing and confirmed their identities as Azotobacter sp. The indigenous Azotobacter strains with multiple PGP activities could be further used for commercial production.

Bacillus subtilis CP4, isolated from native soil in combination with arbuscular mycorrhizal fungi promotes biofortification, yield and metabolite production in wheat under field conditions

AIMS

The aim of this study was to identify the best combination of plant growth promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF) for biofortification and enhancing yield in wheat as well as improve soil health under field conditions. Another aim was to get insights into metabolite dynamics in plants treated with PGPB and AMF.

METHODS AND RESULTS

Different combinations of PGPB and AMF that gave good results in greenhouse study were used in a field study. The combined application of Bacillus subtilis CP4 (native PGPB) and AMF gave the best results with a significant increase in biomass, macronutrient and micronutrient content in wheat grains and improvement in yield-related parameters relative to the untreated control. PGPB and AMF treatment increased antioxidant enzymes and compounds and decreased the level of an oxidation marker. Metabolite profiling performed using Gas Chromatography-Mass Spectrometry (GC-MS) showed significant upregulation of specific organic acids, amino acids, sugars and sugar alcohols in plants treated with CP4 and AMF. The altered pathways due to CP4 and AMF inoculation mainly belong to carbohydrate and amino acid metabolism. A positive correlation was observed between some organic acids, sugars and amino acids with wheat growth and yield parameters. The activities of soil enzymes increased significantly with the best results shown by native PGPB and AMF combination.

CONCLUSIONS

A native bacterial isolate Bacillus subtilis CP4 in combination with AMF showed exceptional ability for biofortification and yield enhancement under field conditions. The upregulation of a number of metabolites showed correlation plant growth promotion and nutrients.

SIGNIFICANCE AND IMPACT OF THE STUDY

The combined application of native B. subtilis CP4 and AMF could offer a more sustainable approach for the development of a biofertilizer to enhance wheat nutrient content and production and soil health thereby advancing agriculture.

Unlocking the potential of plant growth-promoting rhizobacteria on soil health and the sustainability of agricultural systems

The concept of soil health refers to specific soil properties and the ability to support and sustain crop growth and productivity, while maintaining long-term environmental quality. The key components of healthy soil are high populations of organisms that promote plant growth, such as the plant growth promoting rhizobacteria (PGPR). PGPR plays multiple beneficial and ecological roles in the rhizosphere soil. Among the roles of PGPR in agroecosystems are the nutrient cycling and uptake, inhibition of potential phytopathogens growth, stimulation of plant innate immunity, and direct enhancement of plant growth by producing phytohormones or other metabolites. Other important roles of PGPR are their environmental cleanup capacities (soil bioremediation). In this work, we review recent literature concerning the diverse mechanisms of PGPR in maintaining healthy conditions of agricultural soils, thus reducing (or eliminating) the toxic agrochemicals dependence. In conclusion, this review provides comprehensive knowledge on the current PGPR basic mechanisms and applications as biocontrol agents, plant growth stimulators and soil rhizoremediators, with the final goal of having more agroecological practices for sustainable agriculture.

Isolation and characterization of plant growth-promoting endophytic bacteria Bacillus stratosphericus LW-03 from Lilium wardii

In the present study, a new strain of Bacillus stratosphericus LW-03 was isolated from the bulbs of Lilium wardii. The isolated endophytic strain LW-03 exhibited excellent antifungal activity against common plant pathogens, such as Fusarium oxysporum, Botryosphaeria dothidea, Botrytis cinerea, and Fusarium fujikuroi. The growth inhibition percentage of Botryosphaeria dothidea was 74.56 ± 2.35%, which was the highest, followed by Botrytis cinerea, Fusarium fujikuroi, and Fusarium oxysporum were 71.91 ± 2.87%, 69.54 ± 2.73%, and 65.13 ± 1.91%, respectively. The ethyl acetate fraction revealed a number of bioactive compounds and several of which were putatively identified as antimicrobial agents, such as 4-hydroxy-2-nonenylquinoline N-oxide, sphingosine ceramides like cer(d18:0/16:0(2OH)), cer(d18:0/16:0), and cer(d18:1/0:0), di-peptides, tri-peptide, cyclopeptides [cyclo(D-Trp-L-Pro)], [cyclo (Pro-Phe)], dehydroabietylamine, oxazepam, 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine like compound (PC(0:0/20:4), phosphatidylethanolamine (PE(18:1/0:0)), 3-Hydroxyoctadecanoic acid, 7.alpha.,27-Dihydroxycholesterol, N-Acetyl-d-mannosamine, p-Hydroxyphenyllactic acid, Phytomonic acid, and 2-undecenyl-quinoloin-4 (1H). The LW-03 strain exhibits multiple plant growth-promoting traits, including the production of organic acids, ACC deaminase, indole-3-acetic acid (IAA), siderophores, and nitrogen fixation activity. The beneficial effects of the endophytic strain LW-03 on the growth of two lily varieties were further evaluated under greenhouse conditions. Our results revealed plant growth-promoting activity in inoculated plants relative to non-inoculated control plants. The broad-spectrum antifungal activity and multiple plant growth-promoting properties of Bacillus stratosphericus LW-03 make it an important player in the development of biological fertilizers and sustainable agricultural biological control strategies.

Exploring the efficacy of antagonistic rhizobacteria as native biocontrol agents against tomato plant diseases

As the environmental and health concerns alert the necessity to move towards a sustainable agriculture system, biological approach using indigenous plant growth-promoting rhizobacteria (PGPR) gains a strong impetus in the field of plant disease control. In this context, the present review article addresses the usage of rhizospheric antagonistic bacteria as a suitable alternative to control tomato fungal diseases namely Fusarium wilt and early blight disease. Biological control has been considered to be an eco-friendly, safe and effective method for disease management. The inherent traits of PGPR to antagonize a pathogen through various mechanisms has been investigated extensively to utilize them as potent biocontrol agents (BCA). Hence, the article provides a detailed account on different biocontrol mechanisms displayed by BCA. It is also suggested that the use of bacterial consortium ensures consistent performance by BCA in field conditions. Likewise, this review also deals with the opportunities and obstacles faced during commercialization of these antagonistic bacteria as biocontrol agents in the market.

The Endophytic Bacteria Bacillus velezensis Lle-9, Isolated from Lilium leucanthum, Harbors Antifungal Activity and Plant Growth-Promoting Effects

Bacillus velezensis is an important plant growth-promoting rhizobacterium with immense potential in agriculture development. In the present study, Bacillus velezensis Lle-9 was isolated from the bulbs of Lilium leucanthum. The isolated strain showed antifungal activities against plant pathogens like Botryosphaeria dothidea, Fusarium oxysporum, Botrytis cinerea and Fusarium fujikuroi. The highest percentage of growth inhibition i.e., 68.56±2.35% was observed against Fusarium oxysporum followed by 63.12 ± 2.83%, 61.67 ± 3.39% and 55.82 ± 2.76% against Botrytis cinerea, Botryosphaeria dothidea, and Fusarium fujikuroi, respectively. The ethyl acetate fraction revealed a number of bioactive compounds and several were identified as antimicrobial agents such as diketopiperazines, cyclo-peptides, linear peptides, latrunculin A, 5α-hydroxy-6-ketocholesterol, (R)-S-lactoylglutathione, triamterene, rubiadin, moxifloxacin, 9-hydroxy-5Z,7E,11Z,14Zeicosatetraenoic acid, D-erythro-C18-Sphingosine, citrinin, and 2- arachidonoyllysophosphatidylcholine. The presence of these antimicrobial compounds in the bacterial culture might have contributed to the antifungal activities of the isolated B. velezensis Lle- 9. The strain showed plant growth-promoting traits such as production of organic acids, ACC deaminase, indole-3-acetic acid (IAA), siderophores, and nitrogen fixation and phosphate solubilization. IAA production was accelerated with application of exogenous tryptophan concentrations in the medium. Further, the lily plants upon inoculation with Lle-9 exhibited improved vegetative growth, more flowering shoots and longer roots than control plants under greenhouse condition. The isolated B. velezensis strain Lle-9 possessed broad-spectrum antifungal activities and multiple plant growth-promoting traits and thus may play an important role in promoting sustainable agriculture. This strain could be developed and applied in field experiments in order to promote plant growth and control disease pathogens.

Towards a Sustainable Agriculture: Strategies Involving Phytoprotectants against Salt Stress

Salinity is one of the main constraints for agriculture productivity worldwide. This important abiotic stress has worsened in the last 20 years due to the increase in water demands in arid and semi-arid areas. In this context, increasing tolerance of crop plants to salt stress is needed to guarantee future food supply to a growing population. This review compiles knowledge on the use of phytoprotectants of microbial origin (arbuscular mycorrhizal fungi and plant growth-promoting rhizobacteria), osmoprotectants, melatonin, phytohormones and antioxidant metabolism-related compounds as alleviators of salt stress in numerous plant species. Phytoprotectants are discussed in detail, including their nature, applicability, and role in the plant in terms of physiological and phenotype effects. As a result, increased crop yield and crop quality can be achieved, which in turn positively impact food security. Herein, efforts from academic and industrial sectors should focus on defining the treatment conditions and plant-phytoprotectant associations providing higher benefits.

Comparative analysis of endophytic bacterial diversity between two varieties of sunflower Helianthus annuus with their PGP evaluation

Endophytic bacterial diversity shows an intricate network of interactions with host plants as they reside in various tissues and organs at certain stages or all stages of their life cycle stimulating the plant growth and fitness. Sunflower is a trendy oilfield crop and variation in its varieties is associated with the dynamics of endophytic diversity. The present study is undertaken to identify and compare the ecological niche of endophytic bacterial communities amongst different tissues of two hybrids varieties Hysun-33 and Hysun-39 of sunflower (Helianthus annuus) at three developmental stages which are vegetative stage I (after 15 days of seeds germination), vegetative stage II (after 30 days of germination) and reproductive stage (after 90 days of germination). A total of 74 endophytes from Hysun-33 and 115 endophytes from Hysun-39 have been isolated from different tissues and growth stages. Amongst plant parts, root tissues harbored higher bacterial inhabitants (44) followed by stem (33), leaf (30) and flower (7) of Hysun-39. Likewise, Hysun-33 endophytes colonized roots more abundantly followed by leaves, stem and flowers. All strains are found to be gram positive with the exception of only RA9 from Hysun-33 and RB9 from Hysun-39 that are gram negative. Among different growth stages, the maximum bacterial population (CFU of 320 × 103) was found amongst root microflora at vegetative stage II of plant in Hysun-39 variety as compared to root endophytes of Hysun-33 having (CFU of 10 × 103). The evaluation of their growth promoting features revealed that among 74 isolates of Hysun-33, 70% exhibited the ability of hydrogen cyanide production, 43% IAA production, 36% siderophore production and 4% nitrogen fixation and also phosphate solubilization. However among 115 isolates of Hysun-39, 64% appeared as hydrogen cyanide producers, 56% IAA producers, 33% siderophore producers, 2% nitrogen fixers and 4% as phosphate solubilizers. Therefore our study reveals understanding of wide-ranging diversity of endophytic bacteria and their beneficial relationship with internal tissues of host plant which may recommend their implementation to crops for better development of agricultural systems.